Re: [ccp4bb] pairwise CCano - SUMMARY
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Dear all,
I received three responses to my Email, those two you saw on the BB
and one from Clemens Vonrhein who pointed me at the program
'check_indexing' from the AutoBuster Suite.
I tried both pointless and check_indexing, and both work equally fine.
I did not try Pierre Legrand's solution because I already had two, but
I am convinced it works equally well.
Pointless has the advantage of doing all combinations automatically,
check_indexing has the advantage of the more concise output. Since
check_indexing only relates all input file to the first one, I applied
the following bash-script to get all pairwise combinations, which
repeatedly pops the first mtz-file from the stack until there are only
two left:
#-- 8 snip --
mtzs=(1.mtz \
2.mtz \
3.mtz
)
while (( ${#mtzs[*]} 1 )); do
check_indexing -v ${mtzs[*]}
mtzs=(${mtzs[@]:1})
done
#-snap 8 -
The list of mtz-files can surely be expanded (I used the script with
14 entries).
In my particular case pointless had another important advantage which
gave me a great crystallographic lesson:
The beta-angles of all these mtz-files (spacegroup C2) vary by less
than 0.1 degree about 90degrees. While check_indexing takes all the
crystallographic reindexing possibilities into account, pointless also
realised that in this particular case, the crystallographic convention
of beta90 degrees would render some of the data sets incompatible
with others and therefore reindexed them to beta90degrees. I was
reminded the molecules don't attend lectures in crystallography and
may therefore not obey conventions. In case of a single data set this
is surely no problem, but in this case it was.
Of course XDS would have picked the correct indexing with beta89
degrees if only I had provided the same REFERENCE_DATA_SET to all data
sets, but I did not here, and I had to see the reindexing operator in
the form [-h -k l] from pointless in order to realise what was going on.
Thanks a lot for all three suggestions
Tim
On 03/14/2014 11:14 AM, Phil Evans wrote:
If you assigns them to different datasets in Pointless, then
Aimless will give you the cross-dataset correlations. By default it
will scale them to together first, but you can skip that if you
want
It might not scale well to a large number of files (OK up to about
10 I guess)
Phil
On 14 Mar 2014, at 09:33, Tim Gruene t...@shelx.uni-ac.gwdg.de
wrote:
Dear all,
I am looking for a tool that prints (and preferably plots, e.g. as
postscript) the pairwise anomalous CC vs. resolution for several
input HKL-files. xprep does this, but it is interactive and
requires a fair bit of typing. Since I have a large number of
HKL-files from XDS, I would like to script that and then flip
through the pages of the postscript-plots.
I looked into pointless but could not find even a table.
Since there recently were some publications one the use of many
files for phasing, I though such a tool should exist!?
Best, Tim
- --
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
GPG Key ID = A46BEE1A
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[ccp4bb] pairwise CCano
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear all, I am looking for a tool that prints (and preferably plots, e.g. as postscript) the pairwise anomalous CC vs. resolution for several input HKL-files. xprep does this, but it is interactive and requires a fair bit of typing. Since I have a large number of HKL-files from XDS, I would like to script that and then flip through the pages of the postscript-plots. I looked into pointless but could not find even a table. Since there recently were some publications one the use of many files for phasing, I though such a tool should exist!? Best, Tim - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Icedove - http://www.enigmail.net/ iD8DBQFTIszcUxlJ7aRr7hoRApYyAKDt36pF11DAbkfcXVq+uLjqvm91HgCfSZ+V BVpiCx4q9DZZCqDLenHX374= =itCO -END PGP SIGNATURE-
Re: [ccp4bb] pairwise CCano
Hello Tim :-) You can try to do this with sftools. It is also an interactive type of program input but you can easily calculate correlations. After converting xds files to mtz, you can try some thing like this : sftools eof sftools_1.log READ $mtz1 READ $mtz2 SELECT RESOL 2.8 CORREL COL 5 10 SHELLS 10 eof For the ploting, I'll use gnuplot after parsing the sftools_1.log file. Good luck with this, Cheers, Pierre De : CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] de la part de Tim Gruene [t...@shelx.uni-ac.gwdg.de] Envoyé : vendredi 14 mars 2014 10:33 À : CCP4BB@JISCMAIL.AC.UK Objet : [ccp4bb] pairwise CCano -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear all, I am looking for a tool that prints (and preferably plots, e.g. as postscript) the pairwise anomalous CC vs. resolution for several input HKL-files. xprep does this, but it is interactive and requires a fair bit of typing. Since I have a large number of HKL-files from XDS, I would like to script that and then flip through the pages of the postscript-plots. I looked into pointless but could not find even a table. Since there recently were some publications one the use of many files for phasing, I though such a tool should exist!? Best, Tim - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Icedove - http://www.enigmail.net/ iD8DBQFTIszcUxlJ7aRr7hoRApYyAKDt36pF11DAbkfcXVq+uLjqvm91HgCfSZ+V BVpiCx4q9DZZCqDLenHX374= =itCO -END PGP SIGNATURE-
Re: [ccp4bb] pairwise CCano
If you assigns them to different datasets in Pointless, then Aimless will give you the cross-dataset correlations. By default it will scale them to together first, but you can skip that if you want It might not scale well to a large number of files (OK up to about 10 I guess) Phil On 14 Mar 2014, at 09:33, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear all, I am looking for a tool that prints (and preferably plots, e.g. as postscript) the pairwise anomalous CC vs. resolution for several input HKL-files. xprep does this, but it is interactive and requires a fair bit of typing. Since I have a large number of HKL-files from XDS, I would like to script that and then flip through the pages of the postscript-plots. I looked into pointless but could not find even a table. Since there recently were some publications one the use of many files for phasing, I though such a tool should exist!? Best, Tim - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Icedove - http://www.enigmail.net/ iD8DBQFTIszcUxlJ7aRr7hoRApYyAKDt36pF11DAbkfcXVq+uLjqvm91HgCfSZ+V BVpiCx4q9DZZCqDLenHX374= =itCO -END PGP SIGNATURE-
